Honors & Awards

  • National Cancer Institute and NIH Officer of the Director Scholarship, Keystone Conference (2016)
  • Fayez Sarofim Postdoctoral Fellowship, Damon Runyon Cancer Research Foundation (2013-2017)
  • Martin and Beate Block Award, Aspen Center for Physics (2013)
  • HHMI Undergraduate Research Fellowship, HHMI (2005-2007)

Professional Education

  • Doctor of Philosophy, Massachusetts Institute of Technology (2012)
  • Bachelor of Science, Vanderbilt University (2008)

Stanford Advisors

Current Research and Scholarly Interests

A decade ago, a collection of multi-organ pediatric disorders was attributed to dysfunctional cilia; cell-surface organelles that mediate cell-to-cell communication. These disorders (termed ciliopathies) predispose patients to respiratory inflammation, diabetes, and cancer, and the elucidation of cilia functions inform these prevalent health problems. Reflecting the diverse symptoms of cilia diseases, cilia function throughout the body, and surprisingly, almost every cell type presents at least one cilium. Cilia house receptors and receive signals, but it is not known how signaling is regulated or transduced into the cell. Receptor trafficking provides a molecular entry point to this problem as the receptor mistrafficking is characteristic of ciliopathies. The goal of my research is to determine how receptor trafficking regulates cilia signaling, and to uncover novel roles of cilia in cell-to-cell communication.

1. Receptor Trafficking and Bardet-Biedl Syndrome
The ciliary membrane contains numerous G-protein coupled receptors (GPCRs) that, upon activation, are removed from the cilium. By live-cell imaging of ciliated epithelial cells, I found that two competing pathways remove activated GPCRs from cilia: retrieval back into the cell or secretion into extracellular vesicles. Importantly, in the ciliopathy Bardet-Biedl Syndrome (BBS), both pathways are misregulated. One branch of my research focuses on how BBS-associated proteins regulate receptor trafficking, and how receptor trafficking regulates signaling.

2. Biogenesis of Extracellular Vesicles
A second thrust of my research is to understand how extracellular vesicles are formed. Extracellular vesicles are widely observed in biology, and function both to dispose unwanted molecules and transfer messages to other cells. Mammals release extracellular vesicles by several distinct pathways, yet our molecular understanding is limited to highly-conserved components identified by yeast genetics. Although yeast genetics discovered the important ESCRT cascade, mammals have elaborated and, in some contexts deviated from, this mechanism. For instance, mammalian cells have evolved to use actin for releasing vesicles from cilia, microvilli, and the plasma membrane. Leveraging biochemical tools for studying cilia, I identified a network of actin motors (Myosin 6) and crosslinkers (Drebrin, alpha-Actinin-4) that sever extracellular vesicles from cilia. This research informs how mammals produce extracellular vesicles, and provides molecular tools to determine the physiologic functions of extracellular vesicles.

All Publications

  • An Actin Network Dispatches Ciliary GPCRs into Extracellular Vesicles to Modulate Signaling. Cell Nager, A. R., Goldstein, J. S., Herranz-Pérez, V., Portran, D., Ye, F., Garcia-Verdugo, J. M., Nachury, M. V. 2017; 168 (1-2): 252-263 e14


    Signaling receptors dynamically exit cilia upon activation of signaling pathways such as Hedgehog. Here, we find that when activated G protein-coupled receptors (GPCRs) fail to undergo BBSome-mediated retrieval from cilia back into the cell, these GPCRs concentrate into membranous buds at the tips of cilia before release into extracellular vesicles named ectosomes. Unexpectedly, actin and the actin regulators drebrin and myosin 6 mediate ectosome release from the tip of cilia. Mirroring signal-dependent retrieval, signal-dependent ectocytosis is a selective and effective process that removes activated signaling molecules from cilia. Congruently, ectocytosis compensates for BBSome defects as ectocytic removal of GPR161, a negative regulator of Hedgehog signaling, permits the appropriate transduction of Hedgehog signals in Bbs mutants. Finally, ciliary receptors that lack retrieval determinants such as the anorexigenic GPCR NPY2R undergo signal-dependent ectocytosis in wild-type cells. Our data show that signal-dependent ectocytosis regulates ciliary signaling in physiological and pathological contexts.

    View details for DOI 10.1016/j.cell.2016.11.036

    View details for PubMedID 28017328

  • Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA plus Machine CELL Stinson, B. M., Nager, A. R., Glynn, S. E., Schmitz, K. R., Baker, T. A., Sauer, R. T. 2013; 153 (3): 628-639


    ClpX, a AAA+ ring homohexamer, uses the energy of ATP binding and hydrolysis to power conformational changes that unfold and translocate target proteins into the ClpP peptidase for degradation. In multiple crystal structures, some ClpX subunits adopt nucleotide-loadable conformations, others adopt unloadable conformations, and each conformational class exhibits substantial variability. Using mutagenesis of individual subunits in covalently tethered hexamers together with fluorescence methods to assay the conformations and nucleotide-binding properties of these subunits, we demonstrate that dynamic interconversion between loadable and unloadable conformations is required to couple ATP hydrolysis by ClpX to mechanical work. ATP binding to different classes of subunits initially drives staged allosteric changes, which set the conformation of the ring to allow hydrolysis and linked mechanical steps. Subunit switching between loadable and unloadable conformations subsequently isomerizes or resets the configuration of the nucleotide-loaded ring and is required for mechanical function.

    View details for DOI 10.1016/j.cell.2013.03.029

    View details for Web of Science ID 000318063500015

    View details for PubMedID 23622246

  • Stepwise Unfolding of a beta Barrel Protein by the AAA plus ClpXP Protease JOURNAL OF MOLECULAR BIOLOGY Nager, A. R., Baker, T. A., Sauer, R. T. 2011; 413 (1): 4-16


    In the AAA+ ClpXP protease, ClpX uses the energy of ATP binding and hydrolysis to unfold proteins before translocating them into ClpP for degradation. For proteins with C-terminal ssrA tags, ClpXP pulls on the tag to initiate unfolding and subsequent degradation. Here, we demonstrate that an initial step in ClpXP unfolding of the 11-stranded β barrel of superfolder GFP-ssrA involves extraction of the C-terminal β strand. The resulting 10-stranded intermediate is populated at low ATP concentrations, which stall ClpXP unfolding, and at high ATP concentrations, which support robust degradation. To determine if stable unfolding intermediates cause low-ATP stalling, we designed and characterized circularly permuted GFP variants. Notably, stalling was observed for a variant that formed a stable 10-stranded intermediate but not for one in which this intermediate was unstable. A stepwise degradation model in which the rates of terminal-strand extraction, strand refolding or recapture, and unfolding of the 10-stranded intermediate all depend on the rate of ATP hydrolysis by ClpXP accounts for the observed changes in degradation kinetics over a broad range of ATP concentrations. Our results suggest that the presence or absence of unfolding intermediates will play important roles in determining whether forced enzymatic unfolding requires a minimum rate of ATP hydrolysis.

    View details for DOI 10.1016/j.jmb.2011.07.041

    View details for Web of Science ID 000296038200002

    View details for PubMedID 21821046

  • Loss of the BBSome perturbs endocytic trafficking and disrupts virulence of Trypanosoma brucei PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Langousis, G., Shimogawa, M. M., Saada, E. A., Vashisht, A. A., Spreafico, R., Nager, A. R., Barshop, W. D., Nachury, M. V., Wohlschlegel, J. A., Hill, K. L. 2016; 113 (3): 632-637
  • Coordinated gripping of substrate by subunits of a AAA plus proteolytic machine NATURE CHEMICAL BIOLOGY Iosefson, O., Nager, A. R., Baker, T. A., Sauer, R. T. 2015; 11 (3): 201-U145


    Hexameric ATP-dependent proteases and protein remodeling machines use conserved loops that line the axial pore to apply force to substrates during the mechanical processes of protein unfolding and translocation. Whether loops from multiple subunits act independently or coordinately in these processes is a critical aspect of the mechanism but is currently unknown for any AAA+ machine. By studying covalently linked hexamers of the Escherichia coli ClpX unfoldase bearing different numbers and configurations of wild-type and mutant pore loops, we show that loops function synergistically, and the number of wild-type loops required for efficient degradation is dependent on the stability of the protein substrate. Our results support a mechanism in which a power stroke initiated in one subunit of the ClpX hexamer results in the concurrent movement of all six pore loops, which coordinately grip and apply force to the substrate.

    View details for DOI 10.1038/nchembio.1732

    View details for Web of Science ID 000349840500010

    View details for PubMedID 25599533

  • Structural basis for membrane targeting of the BBSome by ARL6 NATURE STRUCTURAL & MOLECULAR BIOLOGY Mourdo, A., Nager, A. R., Nachury, M. V., Lorentzen, E. 2014; 21 (12): 1035-1041

    View details for DOI 10.1038/nsmb.2920

    View details for Web of Science ID 000345893300006

    View details for PubMedID 25402481

  • The Intraflagellar Transport Protein IFT27 Promotes BBSome Exit from Cilia through the GTPase ARL6/BBS3 DEVELOPMENTAL CELL Liew, G. M., Ye, F., Nager, A. R., Murphy, J. P., Lee, J. S., Aguiar, M., Breslow, D. K., Gygi, S. P., Nachury, M. V. 2014; 31 (3): 265-278
  • Mechanochemical basis of protein degradation by a double-ring AAA plus machine NATURE STRUCTURAL & MOLECULAR BIOLOGY Olivares, A. O., Nager, A. R., Iosefson, O., Sauer, R. T., Baker, T. A. 2014; 21 (10): 871-875


    Molecular machines containing double or single AAA+ rings power energy-dependent protein degradation and other critical cellular processes, including disaggregation and remodeling of macromolecular complexes. How the mechanical activities of double-ring and single-ring AAA+ enzymes differ is unknown. Using single-molecule optical trapping, we determine how the double-ring ClpA enzyme from Escherichia coli, in complex with the ClpP peptidase, mechanically degrades proteins. We demonstrate that ClpA unfolds some protein substrates substantially faster than does the single-ring ClpX enzyme, which also degrades substrates in collaboration with ClpP. We find that ClpA is a slower polypeptide translocase and that it moves in physical steps that are smaller and more regular than steps taken by ClpX. These direct measurements of protein unfolding and translocation define the core mechanochemical behavior of a double-ring AAA+ machine and provide insight into the degradation of proteins that unfold via metastable intermediates.

    View details for DOI 10.1038/nsmb.2885

    View details for Web of Science ID 000342862000006

    View details for PubMedID 25195048

  • Engineering fluorescent protein substrates for the AAA+ Lon protease PROTEIN ENGINEERING DESIGN & SELECTION Wohlever, M. L., Nager, A. R., Baker, T. A., Sauer, R. T. 2013; 26 (4): 299-305


    AAA+ proteases, such as Escherichia coli Lon, recognize protein substrates by binding to specific peptide degrons and then unfold and translocate the protein into an internal degradation chamber for proteolysis. For some AAA+ proteases, attaching specific degrons to the N- or C-terminus of green fluorescent protein (GFP) generates useful substrates, whose unfolding and degradation can be monitored by loss of fluorescence, but Lon fails to degrade appropriately tagged GFP variants at a significant rate. Here, we demonstrate that Lon catalyzes robust unfolding and degradation of circularly permuted variants of GFP with a β20 degron appended to the N terminus or a sul20 degron appended to the C terminus. Lon degradation of non-permuted GFP-sul20 is very slow, in part because the enzyme cannot efficiently extract the degron-proximal C-terminal β-strand to initiate denaturation. The circularly permuted GFP substrates described here allow convenient high-throughput assays of the kinetics of Lon degradation in vitro and also permit assays of Lon proteolysis in vivo.

    View details for DOI 10.1093/protein/gzs105

    View details for Web of Science ID 000316748200007

    View details for PubMedID 23359718

  • Dynamic and static components power unfolding in topologically closed rings of a AAA plus proteolytic machine NATURE STRUCTURAL & MOLECULAR BIOLOGY Glynn, S. E., Nager, A. R., Baker, T. A., Sauer, R. T. 2012; 19 (6): 616-?


    In the Escherichia coli ClpXP protease, a hexameric ClpX ring couples ATP binding and hydrolysis to mechanical protein unfolding and translocation into the ClpP degradation chamber. Rigid-body packing between the small AAA+ domain of each ClpX subunit and the large AAA+ domain of its neighbor stabilizes the hexamer. By connecting the parts of each rigid-body unit with disulfide bonds or linkers, we created covalently closed rings that retained robust activity. A single-residue insertion in the hinge that connects the large and small AAA+ domains and forms part of the nucleotide-binding site uncoupled ATP hydrolysis from productive unfolding. We propose that ATP hydrolysis drives changes in the conformation of one hinge and its flanking domains and that the changes are propagated around the AAA+ ring through the topologically constrained set of rigid-body units and hinges to produce coupled ring motions that power substrate unfolding.

    View details for DOI 10.1038/nsmb.2288

    View details for Web of Science ID 000304958200009

    View details for PubMedID 22562135

  • Glycine Dimerization Motif in the N-terminal Transmembrane Domain of the High Density Lipoprotein Receptor SR-BI Required for Normal Receptor Oligomerization and Lipid Transport JOURNAL OF BIOLOGICAL CHEMISTRY Gaidukov, L., Nager, A. R., Xu, S., Penman, M., Krieger, M. 2011; 286 (21): 18452-18464


    Scavenger receptor class B, type I (SR-BI), a CD36 superfamily member, is an oligomeric high density lipoprotein (HDL) receptor that mediates negatively cooperative HDL binding and selective lipid uptake. We identified in the N-terminal transmembrane (N-TM) domain of SR-BI a conserved glycine dimerization motif, G(15)X(2)G(18)X(3)AX(2)G(25), of which the submotif G(18)X(3)AX(2)G(25) significantly contributes to homodimerization and lipid uptake activity. SR-BI variants were generated by mutations (single or multiple Gly → Leu substitutions) or by replacing the N-TM domain with those from other CD36 superfamily members containing (croquemort) or lacking (lysosomal integral membrane protein (LIMP) II) this glycine motif (chimeras). None of the SR-BI variants exhibited altered surface expression (based on antibody binding) or HDL binding. However, the G15L/G18L/G25L triple mutant exhibited reductions in cell surface homo-oligomerization (>10-fold) and the rate of selective lipid uptake (∼ 2-fold). Gly(18) and Gly(25) were necessary for normal lipid uptake activity of SR-BI and the SR-BI/croquemort chimera. The lipid uptake activity of the glycine motif-deficient SR-BI/LIMP II chimera was low but could be increased by introducing glycines at positions 18 and 25. The rate of lipid uptake mediated by SR-BI/LIMP II chimeras was proportional to the extent of receptor oligomerization. Thus, the glycine dimerization motif G(18)X(3)AX(2)G(25) in the N-TM domain of SR-BI contributes substantially to the homo-oligomerization and lipid transport activity of SR-BI but does not influence the negative cooperativity of HDL binding. Oligomerization-independent binding cooperativity suggests that classic allostery is not involved and that the negative cooperativity is probably the consequence of a "lattice effect" (interligand steric interference accompanying binding to adjacent receptors).

    View details for DOI 10.1074/jbc.M111.229872

    View details for Web of Science ID 000290785700018

    View details for PubMedID 21454587

  • Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA plus Protein-Unfolding Machine CELL Glynn, S. E., Martin, A., Nager, A. R., Baker, T. A., Sauer, R. T. 2009; 139 (4): 744-756


    ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.

    View details for DOI 10.1016/j.cell.2009.09.034

    View details for Web of Science ID 000271747200018

    View details for PubMedID 19914167

  • A dynamic model for replication protein A (RPA) function in DNA processing pathways NUCLEIC ACIDS RESEARCH Fanning, E., Klimovich, V., Nager, A. R. 2006; 34 (15): 4126-4137


    Processing of DNA in replication, repair and recombination pathways in cells of all organisms requires the participation of at least one major single-stranded DNA (ssDNA)-binding protein. This protein protects ssDNA from nucleolytic damage, prevents hairpin formation and blocks DNA reannealing until the processing pathway is successfully completed. Many ssDNA-binding proteins interact physically and functionally with a variety of other DNA processing proteins. These interactions are thought to temporally order and guide the parade of proteins that 'trade places' on the ssDNA, a model known as 'hand-off', as the processing pathway progresses. How this hand-off mechanism works remains poorly understood. Recent studies of the conserved eukaryotic ssDNA-binding protein replication protein A (RPA) suggest a novel mechanism by which proteins may trade places on ssDNA by binding to RPA and mediating conformation changes that alter the ssDNA-binding properties of RPA. This article reviews the structure and function of RPA, summarizes recent studies of RPA in DNA replication and other DNA processing pathways, and proposes a general model for the role of RPA in protein-mediated hand-off.

    View details for DOI 10.1093/nar/gk1550

    View details for Web of Science ID 000240929700011

    View details for PubMedID 16935876